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allow slim to be built from source #52

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28 changes: 24 additions & 4 deletions .github/actions/build-docs/action.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,11 @@ inputs:
required: false
default: 'false'

install-slim-branch:
description: 'Name of github branch to install SLiM from (if not specified, use conda)'
required: false
default: ''

install-playwright:
description: 'Install Playwright (chromium) for docs that render browser screenshots'
required: false
Expand All @@ -44,21 +49,34 @@ runs:
run: sudo apt-get update && sudo apt-get install -y ${ADDITIONAL_APT_PACKAGES}

- name: Set up micromamba
if: ${{ inputs.install-slim == 'true' }}
if: ${{ inputs.install-slim == 'true' }} && ${{ inputs.install-slim-branch == '' }}
uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0

- name: Install SLiM
if: ${{ inputs.install-slim == 'true' }}
if: ${{ inputs.install-slim == 'true' }} && ${{ inputs.install-slim-branch == '' }}
shell: bash
# MAMBA_ROOT_PREFIX is a fixed, controlled path set by setup-micromamba, not attacker-controlled.
run: | # zizmor: ignore[github-env]
micromamba install -n base -y slim
echo "$MAMBA_ROOT_PREFIX/bin" >> $GITHUB_PATH

- name: Install development SLiM
if: ${{ inputs.install-slim == 'true' }} && ${{ inputs.install-slim-branch != '' }}
shell: bash
run: |
git clone https://github.com/messerlab/SLiM.git
mkdir -p SLiM/Release
cd SLiM/Release
git checkout ${{ inputs.install-slim-branch }}
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j 2

- name: Verify SLiM
if: ${{ inputs.install-slim == 'true' }}
shell: bash
run: slim -v
run: |
export PATH=$PWD/SLiM/Release:$PATH
slim -v

- name: Install uv
uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
Expand Down Expand Up @@ -99,4 +117,6 @@ runs:
- name: Build documentation
shell: bash
working-directory: docs
run: make
run: |
export PATH=$PWD/SLiM/Release:$PATH
make
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